Ellis Anderson
5/30/2016
Background slides courtesy of Leslie Herrera, May 2nd 2015
What genes in domesticated tomato are involved in shade avoidance?
Wild-type: Standard for comparison
Mutant of interest: Consitutive elongation
Mutant of interest (tep-1) has petioles that are longer than the control (M82) by the 5th week of development
A bioinformatics approach to find the mutation responsible for the tep-1 phenotype
Run through Leslie's code step by step
Results:
Filtering based on genotype
# Filter to keep rows where M82 = "1/1"
tep_snp_data <-subset(tep_data, tep.gt != "0/0")
tep_snp_data<-tep_snp_data[grep("TYPE=snp", tep_snp_data$INFO),]
tep_snp_data <- tep_snp_data[!is.na(tep_snp_data$tep.read.depth),]
Filtering based on genotype
# Filter to keep rows where M82 = "1/1"
tep_snp_data <-subset(tep_data, tep.gt != "0/0")
tep_snp_data <- tep_snp_data[grepl("1/1",tep_snp_data$M82.gt),]
tep_snp_data<-tep_snp_data[grep("TYPE=snp", tep_snp_data$INFO),]
tep_snp_data <- tep_snp_data[!is.na(tep_snp_data$tep.read.depth),]
SRR404081.fastq.gzS_lycopersicum_chromosomes.2.50.fabwa mempicard-tools functions to add read groups and combine all readsfreebayes to call SNPs for analysis in RAdded additional filtering criteria to remove any Heinz-Heinz polymorphisms
tep_snp_data <- tep_snp_data[grepl("0/0",tep_snp_data$Heinz.gt),]
Chromosome 9:
All Chromosomes:
All Chromosomes:
| Name | Description |
|---|---|
| Solyc09g075980.2 | Os01g0778500 protein |
| Solyc09g075990.2 | IPR002828 Survival protein SurE-like phosphatase/nucleotidase |
| Solyc09g076000.2 | Serine/threonine protein kinase |
| Solyc09g076010.2 | IPR019787 Zinc finger, PHD-finger |
| Solyc09g076020.2 | Imidazoleglycerol-phosphate dehydratase |
| Solyc09g076040.2 | Protein SUPPRESSOR OF GENE SILENCING 3 homolog |
| Solyc09g076050.2 | Frigida-like |
| Solyc09g082060.2 | Cysteine synthase |
| Solyc09g082090.1 | Unknown Protein |
| Solyc09g082080.1 | Plant-specific domain TIGR01568 family protein |
| Name | Description |
|---|---|
| Solyc09g076000.2 | Serine/threonine protein kinase |
| Solyc09g076040.2 | Protein SUPPRESSOR OF GENE SILENCING 3 homolog |
| Solyc09g076010.2 | IPR019787 Zinc finger, PHD-finger |
Wu J, Wang J, Pan C, Guan X, Wang Y, Liu S, et al. (2014) Genome-Wide Identification of MAPKK and MAPKKK Gene Families in Tomato and Transcriptional Profiling Analysis during Development and Stress Response. PLoS ONE 9(7): e103032. doi:10.1371/journal.pone.0103032
Xavier Adenot, Taline Elmayan, Dominique Lauressergues, Stéphanie Boutet, Nicolas Bouché, Virginie Gasciolli, Hervé Vaucheret, DRB4-Dependent TAS3 trans-Acting siRNAs Control Leaf Morphology through AGO7, Current Biology, Volume 16, Issue 9, 9 May 2006, Pages 927-932, ISSN 0960-9822, http://dx.doi.org/10.1016/j.cub.2006.03.035.